Published in Bioinformatics on January 01, 2002
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol (2014) 27.48
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics (2010) 7.78
Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res (2008) 6.15
Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res (2009) 3.30
Statistical implications of pooling RNA samples for microarray experiments. BMC Bioinformatics (2003) 2.52
Application of independent component analysis to microarrays. Genome Biol (2003) 2.16
Statistical methods of background correction for Illumina BeadArray data. Bioinformatics (2009) 1.99
Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization. Genome Biol (2005) 1.80
Modeling gene expression measurement error: a quasi-likelihood approach. BMC Bioinformatics (2003) 1.72
Evaluating different methods of microarray data normalization. BMC Bioinformatics (2006) 1.65
Calibration and assessment of channel-specific biases in microarray data with extended dynamical range. BMC Bioinformatics (2004) 1.58
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Sterile protective immunity to malaria is associated with a panel of novel P. falciparum antigens. Mol Cell Proteomics (2011) 1.53
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Compressive sensing DNA microarrays. EURASIP J Bioinform Syst Biol (2009) 1.41
Comparison of small n statistical tests of differential expression applied to microarrays. BMC Bioinformatics (2009) 1.40
A two-sample Bayesian t-test for microarray data. BMC Bioinformatics (2006) 1.40
Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment. BMC Bioinformatics (2004) 1.35
Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. Silence (2011) 1.35
Baseline correction for NMR spectroscopic metabolomics data analysis. BMC Bioinformatics (2008) 1.35
Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell (2012) 1.29
Spike-in validation of an Illumina-specific variance-stabilizing transformation. BMC Res Notes (2008) 1.28
Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts. PLoS One (2012) 1.27
Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method. BMC Bioinformatics (2006) 1.26
Systems biology approach predicts antibody signature associated with Brucella melitensis infection in humans. J Proteome Res (2011) 1.24
A study of inter-lab and inter-platform agreement of DNA microarray data. BMC Genomics (2005) 1.24
Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets. BMC Bioinformatics (2013) 1.22
Immune profiling with a Salmonella Typhi antigen microarray identifies new diagnostic biomarkers of human typhoid. Sci Rep (2013) 1.20
Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities. Appl Environ Microbiol (2006) 1.17
Making informed choices about microarray data analysis. PLoS Comput Biol (2010) 1.13
State-of-the art data normalization methods improve NMR-based metabolomic analysis. Metabolomics (2011) 1.11
Exploratory differential gene expression analysis in microarray experiments with no or limited replication. Genome Biol (2004) 1.09
Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens. PLoS Negl Trop Dis (2010) 1.08
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Identification of tissue cyst wall components by transcriptome analysis of in vivo and in vitro Toxoplasma gondii bradyzoites. Eukaryot Cell (2011) 1.07
A multivariate prediction model for microarray cross-hybridization. BMC Bioinformatics (2006) 1.07
Pre-erythrocytic antibody profiles induced by controlled human malaria infections in healthy volunteers under chloroquine prophylaxis. Sci Rep (2013) 1.06
Warped linear mixed models for the genetic analysis of transformed phenotypes. Nat Commun (2014) 1.06
Empirical Bayes models for multiple probe type microarrays at the probe level. BMC Bioinformatics (2008) 1.06
Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays. BMC Bioinformatics (2004) 1.06
High-resolution spatial normalization for microarrays containing embedded technical replicates. Bioinformatics (2006) 1.03
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. Nucleic Acids Res (2013) 1.02
A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes. BMC Genomics (2008) 1.02
"Hook"-calibration of GeneChip-microarrays: theory and algorithm. Algorithms Mol Biol (2008) 1.02
Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays. BMC Bioinformatics (2010) 1.00
Functional interactions between the LRP6 WNT co-receptor and folate supplementation. Hum Mol Genet (2010) 1.00
High-throughput profiling of the humoral immune responses against thirteen human papillomavirus types by proteome microarrays. Virology (2010) 0.99
Sub-array normalization subject to differentiation. Nucleic Acids Res (2005) 0.98
Identification of potential serodiagnostic and subunit vaccine antigens by antibody profiling of toxoplasmosis cases in Turkey. Mol Cell Proteomics (2011) 0.98
Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE). BMC Genomics (2010) 0.98
Update for the logicle data scale including operational code implementations. Cytometry A (2012) 0.97
Effect of normalization on statistical and biological interpretation of gene expression profiles. Front Genet (2013) 0.97
Serological profiling of a Candida albicans protein microarray reveals permanent host-pathogen interplay and stage-specific responses during candidemia. PLoS Pathog (2010) 0.96
Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays. BMC Bioinformatics (2004) 0.96
Associating phenotypes with molecular events: recent statistical advances and challenges underpinning microarray experiments. Funct Integr Genomics (2005) 0.96
quantro: a data-driven approach to guide the choice of an appropriate normalization method. Genome Biol (2015) 0.96
Incorporation of gene-specific variability improves expression analysis using high-density DNA microarrays. BMC Biol (2003) 0.94
A comparison on effects of normalisations in the detection of differentially expressed genes. BMC Bioinformatics (2009) 0.93
A review of statistical methods for preprocessing oligonucleotide microarrays. Stat Methods Med Res (2009) 0.92
Discovery of potential diagnostic and vaccine antigens in herpes simplex virus 1 and 2 by proteome-wide antibody profiling. J Virol (2012) 0.92
Measuring similarities between gene expression profiles through new data transformations. BMC Bioinformatics (2007) 0.91
Robust and efficient parameter estimation in dynamic models of biological systems. BMC Syst Biol (2015) 0.89
Importance of replication in analyzing time-series gene expression data: corticosteroid dynamics and circadian patterns in rat liver. BMC Bioinformatics (2010) 0.87
Mining SOM expression portraits: feature selection and integrating concepts of molecular function. BioData Min (2012) 0.87
Immunoproteomic analysis of antibody in lymphocyte supernatant in patients with typhoid fever in Bangladesh. Clin Vaccine Immunol (2013) 0.86
Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution. Biol Direct (2006) 0.86
A universal reference sample derived from clone vector for improved detection of differential gene expression. BMC Genomics (2006) 0.86
Variation in fiberoptic bead-based oligonucleotide microarrays: dispersion characteristics among hybridization and biological replicate samples. Biol Direct (2006) 0.86
cGMP-independent nitric oxide signaling and regulation of the cell cycle. BMC Genomics (2005) 0.86
Measurement of antibody responses to Modified Vaccinia virus Ankara (MVA) and Dryvax(®) using proteome microarrays and development of recombinant protein ELISAs. Vaccine (2011) 0.84
An adaptation of the LMS method to determine expression variations in profiling data. Nucleic Acids Res (2007) 0.84
Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks. BMC Genomics (2012) 0.84
Transcriptional response of ex vivo human skin to ionizing radiation: comparison between low- and high-dose effects. Radiat Res (2011) 0.84
A gene selection method for GeneChip array data with small sample sizes. BMC Genomics (2011) 0.83
Failure of the smallpox vaccine to develop a skin lesion in vaccinia virus-naïve individuals is related to differences in antibody profiles before vaccination, not after. Clin Vaccine Immunol (2012) 0.83
Joint Adaptive Mean-Variance Regularization and Variance Stabilization of High Dimensional Data. Comput Stat Data Anal (2012) 0.82
Biological validation of differentially expressed genes in chronic lymphocytic leukemia identified by applying multiple statistical methods to oligonucleotide microarrays. J Mol Diagn (2005) 0.82
Genomic characterization of a three-dimensional skin model following exposure to ionizing radiation. J Radiat Res (2012) 0.81
PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome. RNA (2015) 0.81
Similarities and differences between two modes of antagonism of the thyroid hormone receptor. ACS Chem Biol (2011) 0.81
Dynamic modeling of gene expression in prokaryotes: application to glucose-lactose diauxie in Escherichia coli. Syst Synth Biol (2011) 0.80
Dissecting early differentially expressed genes in a mixture of differentiating embryonic stem cells. PLoS Comput Biol (2009) 0.80
Challenges for MicroRNA Microarray Data Analysis. Microarrays (Basel) (2013) 0.80
Background adjustment for DNA microarrays using a database of microarray experiments. J Comput Biol (2009) 0.79
Impact of the spotted microarray preprocessing method on fold-change compression and variance stability. BMC Bioinformatics (2011) 0.79
Multivariate hierarchical Bayesian model for differential gene expression analysis in microarray experiments. BMC Bioinformatics (2008) 0.79
Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays. BMC Bioinformatics (2010) 0.78
flowVS: channel-specific variance stabilization in flow cytometry. BMC Bioinformatics (2016) 0.77
Detecting endogenous retrovirus-driven tissue-specific gene transcription. Genome Biol Evol (2015) 0.77
Epithelial, metabolic and innate immunity transcriptomic signatures differentiating the rumen from other sheep and mammalian gastrointestinal tract tissues. PeerJ (2016) 0.77
Quality determination and the repair of poor quality spots in array experiments. BMC Bioinformatics (2005) 0.77
Environmental Interactions and Epistasis Are Revealed in the Proteomic Responses to Complex Stimuli. PLoS One (2015) 0.76
Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals. BMC Bioinformatics (2004) 0.76
A New Distribution Family for Microarray Data. Microarrays (Basel) (2017) 0.75
Automatic selection of preprocessing methods for improving predictions on mass spectrometry protein profiles. AMIA Annu Symp Proc (2010) 0.75
Metabolomic Profiling of Infectious Parapneumonic Effusions Reveals Biomarkers for Guiding Management of Children with Streptococcus pneumoniae Pneumonia. Sci Rep (2016) 0.75
Comparison of pre-processing methods for multiplex bead-based immunoassays. BMC Genomics (2016) 0.75
The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data. Source Code Biol Med (2006) 0.75
A Synthetic Kinome Microarray Data Generator. Microarrays (Basel) (2015) 0.75
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